Geocomputation with R

Introduction

This repository hosts the code underlying Geocomputation with R, a book
by Robin Lovelace, Jakub
Nowosad, and Jannes
Muenchow:

Lovelace, Robin, Jakub Nowosad and Jannes Muenchow (2019).
Geocomputation with R. The R Series. CRC Press.

This book has been published by CRC
Press in the R
Series.
The online version of this book is free to read at
https://geocompr.robinlovelace.net/.

Contributing

We encourage contributions on any part of the book, including:

• Improvements to the text, e.g. clarifying unclear sentences, fixing
  typos (see guidance from Yihui
  Xie).
• Changes to the code, e.g. to do things in a more efficient way.
• Suggestions on content (see the project’s issue
  tracker).

Please see
our-style.md
for the book’s style.

Many thanks to all contributors to the book so far via GitHub (this list
will update automatically): prosoitos,
florisvdh,
katygregg,
erstearns,
eyesofbambi,
tyluRp,
marcosci,
giocomai,
mdsumner,
rsbivand,
pat-s, gisma,
ateucher,
annakrystalli,
kant,
gavinsimpson,
Henrik-P,
Himanshuteli,
yutannihilation,
jbixon13,
katiejolly,
layik, mvl22,
nickbearman,
ganes1410,
richfitz,
SymbolixAU.

During the project we aim to contribute ‘upstream’ to the packages that
make geocomputation with R possible. This impact is recorded in
our-impact.csv.

Reproducing the book

To ease reproducibility, this book is also a package. Installing it from
GitHub will ensure all dependencies to build the book are available on
your computer (you need
remotes):

install.packages("remotes")
remotes::install_github("geocompr/geocompkg")

You need a recent version of the GDAL, GEOS, PROJ and UDUNITS libraries
installed for this to work on Mac and Linux. See the sf package’s
README for information on that.

Once the dependencies have been installed you should be able to build
and view a local version the book with:

bookdown::render_book("index.Rmd") # to build the book
browseURL("_book/index.html") # to view it

Running geocompr code in docker

To ease reproducibility we have set-up a docker image
(robinlovelace/geocompr
on docker hub) containing all the dependencies needed to reproduce the
book. After you have installed
docker and set-it
up on your
computer you
can start a rocker-docker RStudio Server version by running:

docker run -p 8787:8787 -e DISABLE_AUTH=TRUE robinlovelace/geocompr

If it worked you should be able to open-up RStudio server by opening a
browser and navigating to http://localhost:8787/ resulting in an
up-to-date version of R and RStudio running in a container.

On the other hand, you could also start a plain R session running:

docker run -it robinlovelace/geocompr R

To reproduce the entire book in the docker container, you will also need
to mount your local geocompr repository with the following steps
(resulting in output shown below):

# download repo with Windows Powershell or a Unix terminal
git clone https://github.com/Robinlovelace/geocompr.git 
# or download manually from here:
# https://github.com/Robinlovelace/geocompr/archive/master.zip
cd geocompr # navigate into the repo
# on linux and mac:
docker run -d -p 8787:8787 -e DISABLE_AUTH=TRUE -v $(pwd):/home/rstudio/geocompr  robinlovelace/geocompr
# on windows:
docker run -d -p 8787:8787 -v ${pwd}:/home/rstudio/data -e DISABLE_AUTH=TRUE robinlovelace/geocompr

If you see something like this after following the steps above,
congratulations: it worked! See
github.com/rocker-org
for more info.

From this point to build the book you can open projects in the
geocompr directory from the project box in the top-right hand corner,
and knit index.Rmd with the little knit button above the the RStudio
script panel (Ctl+Shift+B should do the same job).

Reproducing this README

To reduce the book’s dependencies, scripts to be run infrequently to
generate input for the book are run on creation of this README.

The additional packages required for this can be installed as follows:

source("code/extra-pkgs.R")

With these additional dependencies installed, you should be able to run
the following scripts, which create content for the book, that we’ve
removed from the main book build to reduce package dependencies and the
book’s build time:

# source("code/cranlogs.R")
# source("code/sf-revdep.R")
# source("code/08-urban-animation.R")
# source("code/08-map-pkgs.R")

Note: the .Rproj file is configured to build a website not a single
page. To reproduce this
README
use the following command:

rmarkdown::render("README.Rmd", output_format = "github_document", output_file = "README.md")

Book statistics

An indication of the book’s progress over time is illustrated below (to
be updated roughly every week as the book progresses).

Book statistics: estimated number of pages per chapter over time.

Citations

To cite packages used in this book we use code from Efficient R
Programming:

# geocompkg:::generate_citations()

This generates .bib and .csv files containing the packages. The current
of packages used can be read-in as follows:

pkg_df = readr::read_csv("extdata/package_list.csv")

Other citations are stored online using Zotero.

If you would like to add to the references, please use Zotero, join the
open group
add your citation to the open geocompr
library.

We use the following citation key format:

[auth:lower]_[veryshorttitle:lower]_[year]

This can be set from inside Zotero desktop with the Better Bibtex plugin
installed (see
github.com/retorquere/zotero-better-bibtex)
by selecting the following menu options (with the shortcut Alt+E
followed by N), and as illustrated in the figure below:

Edit > Preferences > Better Bibtex

Zotero settings: these are useful if you want to add references.

We use Zotero because it is a powerful open source reference manager
that integrates well with the citr package. As described in the
GitHub repo
Robinlovelace/rmarkdown-citr-demo.

References

knitr::kable(pkg_df)